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Khan IU, Saqib M, Amin A, Manzoor S, Ahmed I, Liu RR, Jiao JY, Zhi XY, Li WJ. Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China. Antonie Van Leeuwenhoek 2024; 117:103. [PMID: 39042225 DOI: 10.1007/s10482-024-02001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.
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Affiliation(s)
- Inam Ullah Khan
- Faculty of Veterinary and Animal Sciences, Institute of Microbiology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Muhammad Saqib
- Department of Zoology, Gomal University, Tank Campus, 29050, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Arshia Amin
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 45500, Pakistan
| | - Sadia Manzoor
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Iftikhar Ahmed
- Institute of Microbial Culture Collection of Pakistan (IMCCP), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
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Lee S, Cho M, Sadowsky MJ, Jang J. Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review. J Microbiol 2023; 61:791-805. [PMID: 37594681 DOI: 10.1007/s12275-023-00067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023]
Abstract
Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.
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Affiliation(s)
- Sua Lee
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Min Cho
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Michael J Sadowsky
- BioTechnology Institute, Department of Soil, Water and Climate, and Department of Microbial and Plant Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Jeonghwan Jang
- Division of Biotechnology and Advanced Institute of Environment and Bioscience, Jeonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea.
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Zhong MH, Yang L, Xiong K, Yang HL, Wang XL. Exploring the mechanism of Self-Consistent balance between microbiota and high efficiency in wastewater treatment. BIORESOURCE TECHNOLOGY 2023; 374:128785. [PMID: 36822553 DOI: 10.1016/j.biortech.2023.128785] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Sewage treatment mediated by microbial organisms is a promising green trend. However, the complex balance between microbiota stability and highly efficient wastewater treatment requires investigation. This study successfully improved the effectiveness of sewage treatment by resetting the microbial community structure in the activated sludge. Truepera, Methylophaga, unclassified_Fodinicurvataceae, and unclassified_Actinomanarales were the dominant genera, while salinity and NH3-N content were identified as the key environmental factors governing the microbial structure. By optimizing the microflora structure driven by environmental factors, the key minor genera were activated and coordinated with the aforementioned genera, thereby promoting wastewater treatment. Finally, the chemical oxygen demand, NH3-N, and total phosphorus removal rates were improved to 86.8 ± 1.9%, 82.4 ± 4.1%, and 94.8 ± 3.8%, respectively. It provides a new insight to improve the wastewater treatment through setting microbiota by environmental factor driven.
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Affiliation(s)
- Ming-Hui Zhong
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Lin Yang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Kai Xiong
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Hui-Lin Yang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xiao-Lan Wang
- School of Life Science, Jiangxi Normal University, Nanchang 330022, China.
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Description of five novel thermophilic species of the genus Thermus: Thermus hydrothermalis sp. nov., Thermus neutrinimicus sp. nov., Thermus thalpophilus sp. nov., Thermus albus sp. nov., and Thermus altitudinis sp. nov., isolated from hot spring sediments. Syst Appl Microbiol 2022; 45:126361. [DOI: 10.1016/j.syapm.2022.126361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/27/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022]
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